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For: Gromiha MM, Yugandhar K, Jemimah S. Protein-protein interactions: scoring schemes and binding affinity. Curr Opin Struct Biol 2016;44:31-38. [PMID: 27866112 DOI: 10.1016/j.sbi.2016.10.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/30/2016] [Accepted: 10/25/2016] [Indexed: 01/16/2023]
Number Cited by Other Article(s)
1
Zheng F, Jiang X, Wen Y, Yang Y, Li M. Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength. Comput Struct Biotechnol J 2024;23:460-472. [PMID: 38235359 PMCID: PMC10792694 DOI: 10.1016/j.csbj.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/19/2024]  Open
2
Cai W, Peng S, Tian Y, Bao Y, Liu Q, Dong Y, Liang Z, Liu Q, Ren Y, Ding P, Liu J, Xu T, Li Y. Hydrophobic core evolution of major histocompatibility complex class I chain-related protein A for dramatic enhancing binding affinity. Int J Biol Macromol 2024;271:132588. [PMID: 38788878 DOI: 10.1016/j.ijbiomac.2024.132588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
3
Nikam R, Jemimah S, Gromiha MM. DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein-protein complexes upon mutation. Bioinformatics 2024;40:btae309. [PMID: 38718170 PMCID: PMC11112046 DOI: 10.1093/bioinformatics/btae309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/08/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024]  Open
4
Tong H, Yang T, Xu S, Li X, Liu L, Zhou G, Yang S, Yin S, Li XJ, Li S. Huntington's Disease: Complex Pathogenesis and Therapeutic Strategies. Int J Mol Sci 2024;25:3845. [PMID: 38612657 PMCID: PMC11011923 DOI: 10.3390/ijms25073845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]  Open
5
Tandiana R, Barletta GP, Soler MA, Fortuna S, Rocchia W. Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions. J Chem Theory Comput 2024;20:2630-2642. [PMID: 38445482 DOI: 10.1021/acs.jctc.3c01225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
6
Nikam R, Yugandhar K, Gromiha MM. Deep learning-based method for predicting and classifying the binding affinity of protein-protein complexes. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023;1871:140948. [PMID: 37567456 DOI: 10.1016/j.bbapap.2023.140948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
7
Appadurai R, Koneru JK, Bonomi M, Robustelli P, Srivastava A. Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding. J Chem Theory Comput 2023;19:4711-4727. [PMID: 37338049 PMCID: PMC11108026 DOI: 10.1021/acs.jctc.3c00224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
8
Yang YX, Huang JY, Wang P, Zhu BT. AREA-AFFINITY: A Web Server for Machine Learning-Based Prediction of Protein-Protein and Antibody-Protein Antigen Binding Affinities. J Chem Inf Model 2023. [PMID: 37235532 DOI: 10.1021/acs.jcim.2c01499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
9
Li Z, Zeng M, Geng K, Lai D, Xu Z, Zhou W. Chemical Constituents and Hypoglycemic Mechanisms of Dendrobium nobile in Treatment of Type 2 Diabetic Rats by UPLC-ESI-Q-Orbitrap, Network Pharmacology and In Vivo Experimental Verification. Molecules 2023;28:molecules28062683. [PMID: 36985655 PMCID: PMC10057382 DOI: 10.3390/molecules28062683] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]  Open
10
Harnessing Fc/FcRn Affinity Data from Patents with Different Machine Learning Methods. Int J Mol Sci 2023;24:ijms24065724. [PMID: 36982796 PMCID: PMC10052518 DOI: 10.3390/ijms24065724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/07/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023]  Open
11
Ferraz MVF, Neto JCS, Lins RD, Teixeira ES. An artificial neural network model to predict structure-based protein-protein free energy of binding from Rosetta-calculated properties. Phys Chem Chem Phys 2023;25:7257-7267. [PMID: 36810523 DOI: 10.1039/d2cp05644e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
12
Mai H, Zimmer MH, Miller TF. Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods. J Phys Chem B 2023;127:446-455. [PMID: 36607139 PMCID: PMC9869335 DOI: 10.1021/acs.jpcb.2c05795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/18/2022] [Indexed: 01/07/2023]
13
Jung Y, Geng C, Bonvin AMJJ, Xue LC, Honavar VG. MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules 2023;13:121. [PMID: 36671507 PMCID: PMC9855734 DOI: 10.3390/biom13010121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023]  Open
14
Lee J, Seok C, Ham S, Chong S. Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies. Proteins 2023;91:694-704. [PMID: 36564921 PMCID: PMC9880660 DOI: 10.1002/prot.26458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
15
Harini K, Christoffer C, Gromiha MM, Kihara D. Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server. Methods Mol Biol 2023;2690:355-373. [PMID: 37450159 PMCID: PMC10561630 DOI: 10.1007/978-1-0716-3327-4_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
16
Gurusinghe SN, Oppenheimer B, Shifman JM. Cold spots are universal in protein–protein interactions. Protein Sci 2022;31:e4435. [PMID: 36173158 PMCID: PMC9490803 DOI: 10.1002/pro.4435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/22/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022]
17
In Silico Maturation of a Nanomolar Antibody against the Human CXCR2. Biomolecules 2022;12:biom12091285. [PMID: 36139124 PMCID: PMC9496334 DOI: 10.3390/biom12091285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]  Open
18
CSatDTA: Prediction of Drug–Target Binding Affinity Using Convolution Model with Self-Attention. Int J Mol Sci 2022;23:ijms23158453. [PMID: 35955587 PMCID: PMC9369082 DOI: 10.3390/ijms23158453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 12/10/2022]  Open
19
Williams A, Zhan CG. Fast Prediction of Binding Affinities of SARS-CoV-2 Spike Protein and Its Mutants with Antibodies through Intermolecular Interaction Modeling-Based Machine Learning. J Phys Chem B 2022;126:5194-5206. [PMID: 35817617 PMCID: PMC9301770 DOI: 10.1021/acs.jpcb.2c02123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Indexed: 11/30/2022]
20
Desantis F, Miotto M, Di Rienzo L, Milanetti E, Ruocco G. Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity. Sci Rep 2022;12:12087. [PMID: 35840609 PMCID: PMC9287411 DOI: 10.1038/s41598-022-16338-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022]  Open
21
Fang Z, Peltz G. An automated multi-modal graph-based pipeline for mouse genetic discovery. Bioinformatics 2022;38:3385-3394. [PMID: 35608290 PMCID: PMC9992076 DOI: 10.1093/bioinformatics/btac356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022]  Open
22
The impact of the suppression of highly connected protein interactions on the corona virus infection. Sci Rep 2022;12:9188. [PMID: 35654986 PMCID: PMC9160517 DOI: 10.1038/s41598-022-13373-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/09/2022] [Indexed: 11/28/2022]  Open
23
Kotthoff I, Kundrotas PJ, Vakser IA. Dockground scoring benchmarks for protein docking. Proteins 2022;90:1259-1266. [DOI: 10.1002/prot.26306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/06/2021] [Accepted: 01/21/2022] [Indexed: 11/05/2022]
24
De Lauro A, Di Rienzo L, Miotto M, Olimpieri PP, Milanetti E, Ruocco G. Shape Complementarity Optimization of Antibody–Antigen Interfaces: The Application to SARS-CoV-2 Spike Protein. Front Mol Biosci 2022;9:874296. [PMID: 35669567 PMCID: PMC9163568 DOI: 10.3389/fmolb.2022.874296] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022]  Open
25
Beshnova D, Fang Y, Du M, Sun Y, Du F, Ye J, Chen ZJ, Li B. Computational approach for binding prediction of SARS-CoV-2 with neutralizing antibodies. Comput Struct Biotechnol J 2022;20:2212-2222. [PMID: 35530743 PMCID: PMC9059344 DOI: 10.1016/j.csbj.2022.04.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/03/2022]  Open
26
Zhang J, Fan F, Liu A, Zhang C, Li Q, Zhang C, He F, Shang M. Icariin: A Potential Molecule for Treatment of Knee Osteoarthritis. Front Pharmacol 2022;13:811808. [PMID: 35479319 PMCID: PMC9037156 DOI: 10.3389/fphar.2022.811808] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/21/2022] [Indexed: 01/24/2023]  Open
27
Panday S, Alexov E. Protein-Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation. ACS OMEGA 2022;7:11057-11067. [PMID: 35415339 PMCID: PMC8991903 DOI: 10.1021/acsomega.1c07037] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
28
Williams AH, Zhan CG. Generalized Methodology for the Quick Prediction of Variant SARS-CoV-2 Spike Protein Binding Affinities with Human Angiotensin-Converting Enzyme II. J Phys Chem B 2022;126:2353-2360. [PMID: 35315274 PMCID: PMC8982491 DOI: 10.1021/acs.jpcb.1c10718] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/24/2022] [Indexed: 12/25/2022]
29
Sarnowski CP, Bikaki M, Leitner A. Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins. Structure 2022;30:441-461. [PMID: 35366400 DOI: 10.1016/j.str.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/03/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022]
30
PCA-MutPred: Prediction of binding free energy change upon missense mutation in protein-carbohydrate complexes. J Mol Biol 2022;434:167526. [DOI: 10.1016/j.jmb.2022.167526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/26/2022] [Accepted: 03/01/2022] [Indexed: 11/22/2022]
31
Yang YX, Wang P, Zhu BT. Relative importance of interface and surface areas in protein-protein binding affinity prediction: A machine learning analysis based on linear regression and artificial neural network. Biophys Chem 2022;283:106762. [DOI: 10.1016/j.bpc.2022.106762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 11/02/2022]
32
Zacharias M. Match_Motif: A rapid computational tool to assist in protein-protein interaction design. Protein Sci 2022;31:147-157. [PMID: 34648221 PMCID: PMC8740833 DOI: 10.1002/pro.4208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/12/2022]
33
Renaud N, Geng C, Georgievska S, Ambrosetti F, Ridder L, Marzella DF, Réau MF, Bonvin AMJJ, Xue LC. DeepRank: a deep learning framework for data mining 3D protein-protein interfaces. Nat Commun 2021;12:7068. [PMID: 34862392 PMCID: PMC8642403 DOI: 10.1038/s41467-021-27396-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]  Open
34
Wu N, Jiao L, Bütikofer M, Zeng Z, Zenobi R. High-Mass Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Absolute Quantitation of Noncovalent Protein-Protein Binding Interactions. Anal Chem 2021;93:10982-10989. [PMID: 34328720 DOI: 10.1021/acs.analchem.1c02126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
35
Kurcinski M, Kmiecik S, Zalewski M, Kolinski A. Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations. Int J Mol Sci 2021;22:ijms22147341. [PMID: 34298961 PMCID: PMC8306105 DOI: 10.3390/ijms22147341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/03/2021] [Accepted: 07/04/2021] [Indexed: 12/21/2022]  Open
36
Mishra SK, Cooper CJ, Parks JM, Mitchell JC. Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes. J Phys Chem B 2021;125:6058-6067. [PMID: 34077660 DOI: 10.1021/acs.jpcb.0c11525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
37
Parate S, Rampogu S, Lee G, Hong JC, Lee KW. Exploring the Binding Interaction of Raf Kinase Inhibitory Protein With the N-Terminal of C-Raf Through Molecular Docking and Molecular Dynamics Simulation. Front Mol Biosci 2021;8:655035. [PMID: 34124147 PMCID: PMC8194344 DOI: 10.3389/fmolb.2021.655035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022]  Open
38
Williams AH, Zhan CG. Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. J Phys Chem B 2021;125:4330-4336. [PMID: 33881861 PMCID: PMC8084269 DOI: 10.1021/acs.jpcb.1c00869] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/30/2021] [Indexed: 12/28/2022]
39
Patel D, Patel JS, Ytreberg FM. Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy. J Chem Theory Comput 2021;17:2457-2464. [PMID: 33709712 PMCID: PMC8044032 DOI: 10.1021/acs.jctc.0c01045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
40
Sepahvandi A, Ghaffari M, Bahmanpour AH, Moztarzadeh F, Zarrintaj P, Uludağ H, Mozafari M. COVID-19: insights into virus-receptor interactions. MOLECULAR BIOMEDICINE 2021;2:10. [PMID: 34766003 PMCID: PMC8035060 DOI: 10.1186/s43556-021-00033-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/03/2021] [Indexed: 01/03/2023]  Open
41
Lee W, Park JW, Go YJ, Kim WJ, Rhee YM. Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers. RSC Adv 2021;11:9315-9326. [PMID: 35423456 PMCID: PMC8695334 DOI: 10.1039/d0ra10106k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/23/2021] [Indexed: 11/21/2022]  Open
42
Massoud TF, Paulmurugan R. Molecular Imaging of Protein–Protein Interactions and Protein Folding. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00071-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
43
Gonzalez TR, Martin KP, Barnes JE, Patel JS, Ytreberg FM. Assessment of software methods for estimating protein-protein relative binding affinities. PLoS One 2020;15:e0240573. [PMID: 33347442 PMCID: PMC7751979 DOI: 10.1371/journal.pone.0240573] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/07/2020] [Indexed: 11/19/2022]  Open
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Siebenmorgen T, Zacharias M. Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling. J Chem Inf Model 2020;60:5552-5562. [PMID: 33075222 DOI: 10.1021/acs.jcim.0c00853] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Predicting antibody affinity changes upon mutations by combining multiple predictors. Sci Rep 2020;10:19533. [PMID: 33177627 PMCID: PMC7658247 DOI: 10.1038/s41598-020-76369-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]  Open
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Zhou Y, Zhao R, Schwarz EC, Akbar R, Kaba M, Pattu V, Helms V, Rieger H, Nunes-Hasler P, Qu B. Interorganelle Tethering to Endocytic Organelles Determines Directional Cytokine Transport in CD4+ T Cells. THE JOURNAL OF IMMUNOLOGY 2020;205:2988-3000. [PMID: 33106338 DOI: 10.4049/jimmunol.2000195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 09/20/2020] [Indexed: 12/24/2022]
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Di Rienzo L, Milanetti E, Testi C, Montemiglio LC, Baiocco P, Boffi A, Ruocco G. A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction. Comput Struct Biotechnol J 2020;18:2678-2686. [PMID: 33101606 PMCID: PMC7548301 DOI: 10.1016/j.csbj.2020.09.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/24/2022]  Open
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Jemimah S, Sekijima M, Gromiha MM. ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification. Bioinformatics 2020;36:1725-1730. [PMID: 31713585 DOI: 10.1093/bioinformatics/btz829] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/23/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022]  Open
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Insights into changes in binding affinity caused by disease mutations in protein-protein complexes. Comput Biol Med 2020;123:103829. [DOI: 10.1016/j.compbiomed.2020.103829] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 01/11/2023]
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Savojardo C, Martelli PL, Casadio R. Protein–Protein Interaction Methods and Protein Phase Separation. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-011720-104428] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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